Conformer generation with OMEGA: learning from the data set and the analysis of failures
PCD Hawkins, A Nicholls - Journal of chemical information and …, 2012 - ACS Publications
We recently published a high quality validation set for testing conformer generators,
consisting of structures from both the PDB and the CSD (Hawkins, PCD et al. J. Chem. Inf …
consisting of structures from both the PDB and the CSD (Hawkins, PCD et al. J. Chem. Inf …
Freely available conformer generation methods: how good are they?
Conformer generation has important implications in cheminformatics, particularly in
computational drug discovery where the quality of conformer generation software may affect …
computational drug discovery where the quality of conformer generation software may affect …
Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database
Here, we present the algorithm and validation for OMEGA, a systematic, knowledge-based
conformer generator. The algorithm consists of three phases: assembly of an initial 3D …
conformer generator. The algorithm consists of three phases: assembly of an initial 3D …
Benchmarking commercial conformer ensemble generators
NO Friedrich, C de Bruyn Kops… - Journal of chemical …, 2017 - ACS Publications
We assess and compare the performance of eight commercial conformer ensemble
generators (ConfGen, ConfGenX, cxcalc, iCon, MOE LowModeMD, MOE Stochastic, MOE …
generators (ConfGen, ConfGenX, cxcalc, iCon, MOE LowModeMD, MOE Stochastic, MOE …
Better informed distance geometry: using what we know to improve conformation generation
S Riniker, GA Landrum - Journal of chemical information and …, 2015 - ACS Publications
Small organic molecules are often flexible, ie, they can adopt a variety of low-energy
conformations in solution that exist in equilibrium with each other. Two main search …
conformations in solution that exist in equilibrium with each other. Two main search …
Conformator: a novel method for the generation of conformer ensembles
NO Friedrich, F Flachsenberg, A Meyder… - Journal of chemical …, 2019 - ACS Publications
Computer-aided drug design methods such as docking, pharmacophore searching, 3D
database searching, and the creation of 3D-QSAR models need conformational ensembles …
database searching, and the creation of 3D-QSAR models need conformational ensembles …
CAESAR: a new conformer generation algorithm based on recursive buildup and local rotational symmetry consideration
J Li, T Ehlers, J Sutter, S Varma-O'Brien… - Journal of chemical …, 2007 - ACS Publications
A highly efficient conformer search algorithm based on a divide-and-conquer and recursive
conformer build-up approach is presented in this paper. This approach is combined with …
conformer build-up approach is presented in this paper. This approach is combined with …
Confab-Systematic generation of diverse low-energy conformers
NM O'Boyle, T Vandermeersch, CJ Flynn… - Journal of …, 2011 - Springer
Background Many computational chemistry analyses require the generation of conformers,
either on-the-fly, or in advance. We present Confab, an open source command-line …
either on-the-fly, or in advance. We present Confab, an open source command-line …
Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand …
J Kirchmair, G Wolber, C Laggner… - Journal of chemical …, 2006 - ACS Publications
In continuation of our studies to evaluate the ability of various conformer generators to
produce bioactive conformations, we present the extension of our work on the analysis of …
produce bioactive conformations, we present the extension of our work on the analysis of …
Improving conformer generation for small rings and macrocycles based on distance geometry and experimental torsional-angle preferences
S Wang, J Witek, GA Landrum… - Journal of chemical …, 2020 - ACS Publications
The conformer generator ETKDG is a stochastic search method that utilizes distance
geometry together with knowledge derived from experimental crystal structures. It has been …
geometry together with knowledge derived from experimental crystal structures. It has been …